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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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Talwar C, Singh AK, Choksket S, Korpole S, Lal R, Negi RK. Salinicoccus cyprini sp. nov., isolated from the gut of mirror carp, Cyprinus carpio var. specularis. Int J Syst Evol Microbiol 2020; 70:4111-4118. [PMID: 32538739 DOI: 10.1099/ijsem.0.004247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel orange to pink coloured bacterial strain designated as CT19T was isolated from the gastrointestinal tract of mirror carp, Cyprinus carpio var. specularis (Lacepède, 1803) collected from the Gobind Sagar reservoir at village Lathiani, Una, Himachal Pradesh, India. Cells of the strain were found to be aerobic, Gram-stain-positive, non-motile and non-spore-forming coccoids. Based on the 16S rRNA gene sequence, the strain was closely related to Salinicoccus hispanicus J-82T (=DSM 5352T; 97.4 %), followed by S. sesuvii CC-SPL15-2T (=DSM 23267T; 96.4 %), S. amylolyticus JC304T (=KCTC 33661T; 95.6 %) and S. roseus DSM 5351T (95.4 %). Identity with all other members of the genus were <94.5 %. The draft genome of strain CT19T was assembled to 2.4 Mbp with a G+C content of 47.9 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between strain CT19T and S. hispanicus J-82T were found to be 85.9 and 31.3% respectively which is far below the threshold for species delineation. Iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, C16 : 0 and anteiso-C17 : 0 were the major cellular fatty acids of strain CT19T. Major polar lipids were diphosphatidylglycerol, phosphatidylgylcerol and an unidentified glycolipid. Respiratory quinone system was composed of menaquinone-6 and major cell wall amino acid was l-lysine. Based on phylogenomic, physiological and biochemical characteristics, strain CT19T represents a novel species of the genus Salinicoccus for which the name Salinicoccus cyprini sp. nov. is proposed. The type strain is CT19T (=KCTC 43022T =CCM 8886T=MCC 3834T).
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Affiliation(s)
- Chandni Talwar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Amit Kumar Singh
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Stanzin Choksket
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Rup Lal
- NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
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Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters. Appl Microbiol Biotechnol 2017; 101:7249-7258. [PMID: 28795221 DOI: 10.1007/s00253-017-8428-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/10/2017] [Accepted: 07/17/2017] [Indexed: 01/27/2023]
Abstract
Salinicoccus salsiraiae IM408 (=CGMCC13032) is a novel halophilic bacterium that we isolated from the saline soil of Da Gang Oilfield. It tolerates 60 g/l sodium chloride and up to 123 g/l (1.5 M) sodium acetate and has shown a potential application in bioremediation of wastewater with high salt and high chemical oxygen demand (COD). Two plasmids, pS408-1 and pS408-2, were identified in S. salsiraiae IM408, and the sequences and copy numbers of the plasmids were determined. Based on these plasmids, two shuttle vectors containing a replicon for Escherichia coli, ampicillin, and chloramphenicol resistance genes, as well as the replicon from pS408-1 or pS408-2, were constructed and named as pTCS101 and pTCS201, respectively. A suitable host strain, named S. salsiraiae PE01, was also developed from the wild-type by plasmid elimination. Using the plasmid pTCS101 as an expression vector, L-lactate dehydrogenase from Staphylococcus aureus was expressed successfully in S. salsiraiae PE01. This is the first gene expression system for the Salinicoccus genus. It has provided the potential for expression of desired proteins or for establishment of desired pathways in Salinicoccus strains, which would make these halophiles more advantageous in future biotechnological applications.
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Mevada V, Patel S, Pandya J, Joshi H, Patel R. Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat. GENOMICS DATA 2017; 13:30-34. [PMID: 28702355 PMCID: PMC5485554 DOI: 10.1016/j.gdata.2017.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 02/03/2023]
Abstract
Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp identified by with second largest size for Salinicoccus sp. reported in the NCBI genome database. A total of 652 degradative pathways were identified by KEGG map analysis. Comparative genomic analysis revealed Salinicoccus sp. BAB 3246 as most highly related to Salinicoccus halodurans H3B36. Data mining identified stress response genes and operator pathway for degradation of various environmental pollutants. Annotation data and analysis indicate potential use in pollution control in industrial influent and saline environment.
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Affiliation(s)
- Vishal Mevada
- Shri Sarvajanik Science College, Sarvajanik Campus, Mehsana, India
| | - Shradhdha Patel
- Department of Life Sciences, Hem. North Gujarat University, Patan, India
| | - Jignesh Pandya
- Department of Life Sciences, Hem. North Gujarat University, Patan, India
| | - Himani Joshi
- Department of Life Sciences, Hem. North Gujarat University, Patan, India
| | - Rajesh Patel
- Department of Life Sciences, Hem. North Gujarat University, Patan, India
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Li Y, Wang SK, Xue H, Chang JP, Guo LM, Yang XQ. Corticicoccus populi gen. nov., sp. nov., a member of the family Staphylococcaceae, isolated from symptomatic bark of Populus × euramericana canker. Int J Syst Evol Microbiol 2017; 67:789-794. [DOI: 10.1099/ijsem.0.001602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Sheng-kun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Han Xue
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Ju-pu Chang
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Li-min Guo
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Xu-qi Yang
- Puyang Academy of Forestry, Puyang 457000, PR China
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Srinivas A, Divyasree B, Tushar L, Suresh G, Sasikala C, Ramana CV. Salinicoccus amylolyticus sp. nov., isolated from a saltern. Int J Syst Evol Microbiol 2016; 66:3814-3820. [PMID: 27381021 DOI: 10.1099/ijsem.0.001270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).
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Affiliation(s)
- A Srinivas
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - B Divyasree
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - L Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
| | - G Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
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Kumar RM, Kaur G, Kumar N, Kumar A, Singh NK, Bala M, Kaur N, Mayilraj S. Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2016; 65:3794-3799. [PMID: 26956594 DOI: 10.1099/ijsem.0.000495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, coccoid, halotolerant bacterial strain, designated SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurred at temperatures in the range 25-37 °C (optimum 30 °C), at pH 7.0-11.0 (optimum pH 8.0) and at NaCl concentrations of up to 25.0% (optimum 15.0%). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6%) followed by Salinicoccus halodurans W24T (96.6%). The predominant polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 and anteiso-C17:0. The draft genome of strain SV-16T consisted of 2,591,284 bp with a DNA G+C content of 48.7 mol%. On the basis of the phenotypic characteristics and genotypic distinctiveness of strain SV-16T, it should be classified within a novel species of the genus Salinicoccus, for which the name Salinicoccus sediminis sp. nov. is proposed. The type strain is SV-16T ( = MTCC 11832T = DSM 28797T).
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Affiliation(s)
- Rajendran Mathan Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Narender Kumar
- Division of protein science & Engineering, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Nitin Kumar Singh
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Monu Bala
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Navjot Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
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Hyun DW, Whon TW, Cho YJ, Chun J, Kim MS, Jung MJ, Shin NR, Kim JY, Kim PS, Yun JH, Lee J, Oh SJ, Bae JW. Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)). Stand Genomic Sci 2013; 8:255-63. [PMID: 23991257 PMCID: PMC3746416 DOI: 10.4056/sigs.3967649] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.
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Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Yong-Joon Cho
- ChunLab, Inc., Seoul National University, Seoul, Republic of Korea
| | - Jongsik Chun
- ChunLab, Inc., Seoul National University, Seoul, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Joon-Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Jina Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Republic of Korea
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Brown BP, Brown SR, Senko JM. Microbial communities associated with wet flue gas desulfurization systems. Front Microbiol 2012; 3:412. [PMID: 23226147 PMCID: PMC3510643 DOI: 10.3389/fmicb.2012.00412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/14/2012] [Indexed: 02/01/2023] Open
Abstract
Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.
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Affiliation(s)
- Bryan P Brown
- Department of Biology, The University of Akron, Akron OH, USA
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Kämpfer P, Arun AB, Busse HJ, Young CC, Lai WA, Rekha PD, Chen WM. Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum. Int J Syst Evol Microbiol 2011; 61:2348-2352. [PMID: 21037029 DOI: 10.1099/ijs.0.027524-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T = CCM 7756T).
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Affiliation(s)
- P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - A. B. Arun
- Yenepoya Research Center, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka, India
| | - H.-J. Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - W.-A. Lai
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - P. D. Rekha
- Yenepoya Research Center, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka, India
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
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Qu Z, Li Z, Zhang X, Zhang XH. Salinicoccus qingdaonensis sp. nov., isolated from coastal seawater during a bloom of green algae. Int J Syst Evol Microbiol 2011; 62:545-549. [PMID: 21498663 DOI: 10.1099/ijs.0.030551-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, white-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, strictly aerobic coccus, designated strain ZXM223(T), was isolated from a seawater sample collected from the coast of Qingdao, PR China, during a green algal bloom. It grew at pH 6.0-10.5 and 0-25.0% (w/v) NaCl, with optimum growth at pH 8.5 and 3.0% (w/v) NaCl. Growth occurred at 16-42 °C (optimum at 28 °C). The major fatty acids were anteiso-C(15:0) and iso-C(15:0). Menaquinone 6 (MK-6) was the major respiratory quinone. The polar lipids were phosphatidylglycerol, three unidentified phospholipids and two unknown glycolipids. The peptidoglycan type was L-Lys-Gly(5-6.) The genomic DNA G+C content was 43.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain ZXM223(T) within the genus Salinicoccus, with sequence similarity of 92.2-97.1% between ZXM223(T) and the type strains of this genus. The closest relatives were Salinicoccus kunmingensis YIM Y15(T), 'S. salitudinis' YIM-C678 and S. alkaliphilus T8(T). The DNA-DNA relatedness between strain ZXM223(T) and S. kunmingensis CGMCC 1.6302(T) and 'S. salitudinis' CGMCC 1.6299 (=YIM-C678) was 37±3 and 30±2%, respectively. The phenotypic, chemotaxonomic and phylogenetic characteristics and low DNA-DNA relatedness support the proposal of a novel species of the genus Salinicoccus, Salinicoccus qingdaonensis sp. nov., with the type strain ZXM223(T) (=LMG 24855(T) =CGMCC 1.8895(T)).
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Affiliation(s)
- Zhe Qu
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Zhao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiuming Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
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Bioprospecting microbial natural product libraries from the marine environment for drug discovery. J Antibiot (Tokyo) 2010; 63:415-22. [PMID: 20606699 DOI: 10.1038/ja.2010.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.
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Gao M, Wang L, Chen SF, Zhou YG, Liu HC. Salinicoccus kekensis sp. nov., a novel alkaliphile and moderate halophile isolated from Keke Salt Lake in Qinghai, China. Antonie van Leeuwenhoek 2010; 98:351-7. [PMID: 20449768 DOI: 10.1007/s10482-010-9449-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 04/20/2010] [Indexed: 11/27/2022]
Abstract
A novel alkaliphilic and moderate halophilic bacterium, designated strain K164(T), was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 2.0-20.0% (w/v) NaCl, at 4-50 degrees C and pH 6.5-11.5, with an optimum of 8% (w/v) NaCl, 37degrees C and pH 10, respectively. The predominant respiratory quinone was menaquinone 6 (MK-6) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were anteiso-C(15:0) and iso-C(15:0). The genomic DNA G+C content was 50.16 mol. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K164(T) was a member of the genus Salinicoccus. Strain K164(T) showed the highest similarity (98.4%) with Salinicoccus alkaliphilus AS 1.2691(T) and below 97% similarity with other recognized members of the genus in 16S rRNA gene sequence. Level of DNA-DNA relatedness between strain K164(T) and Salinicoccus alkaliphilus AS 1.2691(T) was 20.1%. On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain K164(T) is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccus kekensis sp. nov. is proposed. The type strain is K164(T) (=CGMCC 1.10337(T) = DSM 23173(T)).
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Affiliation(s)
- Miao Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
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Jung MJ, Kim MS, Roh SW, Shin KS, Bae JW. Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented seafood. Int J Syst Evol Microbiol 2009; 60:653-658. [PMID: 19656926 DOI: 10.1099/ijs.0.012047-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, moderately halophilic bacterium belonging to the genus Salinicoccus was isolated from crabs preserved in soy sauce: a traditional Korean fermented seafood. Colonies of strain Crm(T) were ivory and the cells were non-motile, Gram-positive cocci. The organism was non-sporulating, catalase-positive and oxidase-negative. The major fatty acids of strain Crm(T) were iso-C(15 : 0) (22.0 %), anteiso-C(15 : 0) (40.6 %) and anteiso-C(17 : 0) (12.1 %). The cell wall peptidoglycan contained lysine and glycine, and the major isoprenoid quinone was MK-6. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 47.8 mol%. Strain Crm(T) was closely related to the type strain of Salinicoccus halodurans, with which it shared 96.9 % 16S rRNA gene sequence similarity. The DNA-DNA hybridization value between strains Crm(T) and S. halodurans DSM 19336(T) was 7.6 %. Based on phenotypic, genetic and phylogenetic data, strain Crm(T) should be classified as a novel species within the genus Salinicoccus , for which the name Salinicoccus carnicancri sp. nov. is proposed. The type strain is Crm(T) (=KCTC 13301(T) =JCM 15796(T)).
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Affiliation(s)
- Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Min-Soo Kim
- UST, Biological Resources Center, KRIBB, Daejeon 305-806, Korea.,Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Seong Woon Roh
- UST, Biological Resources Center, KRIBB, Daejeon 305-806, Korea.,Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
| | - Kee-Sun Shin
- UST, Biological Resources Center, KRIBB, Daejeon 305-806, Korea
| | - Jin-Woo Bae
- UST, Biological Resources Center, KRIBB, Daejeon 305-806, Korea.,Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea
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